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Process the raw data

preprocess_bulk_coexp.Rd

Function to do general pre-processing on top of the BulkCoExp(). Options to do scaling, HVG selection, etc.

Usage

preprocess_bulk_coexp(
  object,
  hvg = NULL,
  mad_threshold = NULL,
  scaling = FALSE,
  scaling_type = c("normal", "robust"),
  .verbose = TRUE
)

Arguments

object

The underlying class, see BulkCoExp().

hvg

Integer or float. If an integer, the top hvg genes will be included; if float, the float has to be between 0 and 1, representing the percentage of genes to include.

mad_threshold

Float. Instead of of selecting number or proportion of genes, you can also provide a mad_threshold.

scaling

Boolean. Shall the data be scaled.

scaling_type

String. You have the option to use normal scaling or robust scaling.

.verbose

Boolean. Controls the verbosity of the function.

Value

Returns the class with the processed_data data slot populated and applied parameters added to the params slot.